Molecular modeling, docking and dynamic simulations of growth hormone receptor (GHR) of <i>Labeo rohita</i>

Dhandare, Bhushan C; Rather, Mohd Ashraf; Bhosale, B P; Pawar, R. A.; Guttula, Praveen Kumar; Pagarkar, A. U.

doi:10.1080/07391102.2020.1844063

Cited by 12 publications

(3 citation statements)

References 44 publications

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“…Upon binding, ghr initiates a phosphorylation cascade that regulates signaling and gene expression, ultimately regulating various physiological functions such as growth, metabolism, appetite, reproduction, and social behavior [33,34]. Based on a study of Rohu (Labeo rohita), it was found that several molecules have agonistic effects on the growth hormone receptor protein, and these molecules can be utilized to enhance ray-finned fish growth [35]. tnni2 is a member of the troponin I gene family that encodes a fast-twitch skeletal muscle protein.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome Analysis Reveals Differences in Gene Expression in the Muscle of the Brown-Marbled Grouper (Epinephelus fuscoguttatus) with Different Growth Rates

Wang

Yang

Gong

et al. 2023

Fishes

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Brown-marbled grouper is one of the most important mariculture species in China and is widely used as a crossbreeding parent in the grouper industry. Enhancing growth rates is a key target in fish breeding, and gaining insight into the underlying mechanisms responsible for growth differences between individuals can aid in the improvement of grouper growth rates. However, the mechanism behind growth differences in this fish remains unclear. We analyzed the transcriptome profiles of muscle tissues between fast- and slow-growing brown-marbled grouper using RNA-seq and identified 77 significantly up-regulated genes and 92 significantly down-regulated genes in the extreme growth groups. Our findings suggest that up-regulated genes such as ghr and tnni2, as well as down-regulated genes such as stc2 and pdp1, are associated with growth advantages in brown-marbled grouper. We used differentially expressed genes (DEGs) for GO and KEGG enrichment analyses. The results of the GO enrichments showed that the significantly up-regulated genes in the fast-growing group were involved in protein folding, the actin cytoskeleton, the myosin complex, and other processes. The results of the KEGG enrichments showed that the significantly up-regulated genes in the fast-growing group were involved in various pathways such as glycolysis/gluconeogenesis, adipocytokine signaling, MAPK signaling, carbon metabolism, and PI3K-Akt signaling. Additionally, gene set enrichment analysis (GSEA) showed that the PI3K/AKT/mTOR pathway was up-regulated in the fast-growing group, which may be responsible for the higher nutrient absorption efficiency and muscle growth in these fish. Our results contribute to a better understanding of the molecular mechanisms and regulatory pathways underlying fast growth in brown-marbled grouper. However, further studies are necessary to fully elucidate the mechanisms behind growth differences between individuals.

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Section: Discussionmentioning

confidence: 99%

Transcriptome Analysis Reveals Differences in Gene Expression in the Muscle of the Brown-Marbled Grouper (Epinephelus fuscoguttatus) with Different Growth Rates

Wang

Yang

Gong

et al. 2023

Fishes

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“…However, recently the role of structural bioinformatics, especially in the studies of Protein and RNA modeling, is getting stronger in the observation of the molecular aspect of Fisheries sciences (Hauser and Seeb 2008;Dhandare et al 2020). It is already transcended beyond the frontiers of fish transcriptomics research and entering the realm of 3D biomolecules modeling (Liang et al, 2010;QianXi et al 2014).…”

Section: Discussionmentioning

confidence: 99%

The Structural Annotations of The Mir-122 Non-Coding RNA from The Tilapia Fish (Oreochromis niloticus)

Parikesit

Imron²,

Nurdiansyah

et al. 2022

HAYATI J Biosci

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Tilapia (Oreochromis niloticus) is an important fisheries commodity. Scientific efforts have been done to increase its quality. One of them is staging a premium diet such as a fat-enriched diet. The transcriptomics approach is able to provide the signatures of the diet outcomes by observing the micro(mi)RNA signature in transcriptional regulation. Hence, it was found that the availability of mir-122 is essential in the regulation of a high-fat diet in tilapia. However, this transcriptomics signature is lacking structural annotations and the complete interaction annotations with its silencing(si)RNA. RNAcentral website was navigated for the latest annotation of mir-122 from tilapia and other species as a comparison. MEGA X was employed to comprehend the miRNA evolutionary repertoire. The RNA secondary structure prediction tools from the Vienna RNA package and the RNA tertiary structure prediction tools from simRNA and modeRNA are secured with default parameters. The HNADOCK tools were leveraged to observe the interaction between mir-122 and its siRNA. The post-processing was conducted with the Chimera visualization tool. The secondary and tertiary structure of the mir-122 and its siRNA could be elucidated, docked, and visualized. In this end, further effort to develop a comprehensive molecular breeding tool could be secured with the structural annotation information.

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“…It gives an insight into the underlying characteristics of proteins and is used to predict the three-dimensional structure (3D). Moreover molecular docking are essential method to identify the effect of hazardous ligands or chemicals by recognizing patterns of inter-molecular interactions with the desired proteins (Dhandare et al 2020).…”

Section: Introductionmentioning

confidence: 99%

Homology Modelling, In Silico Prediction And Characterization Of Cytochrome c oxidase In Cyprinus carpio And Tubifex tubifex And Molecular Docking Studies Between The Modelled Protein And Three Commonly Used Surfactants Sodium Dodecyl Sulphate, Cetylpyridinium Chloride And Sodium Laureth Sulphate

Bhattacharya

Daoud

Chatterjee

et al. 2021

Preprint

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The purpose of this work is to evaluate the homology modeling, in silico prediction, and characterisation of Cytochrome c oxidase from Cyprinus carpio and Tubifex tubifex, as well as molecular docking experiments between the modelled protein and three frequently used surfactants. Using the template crystal structure of bovine heart Cytochrome c oxidase, homology modeling of Cytochrome c oxidase (Subunit 2) of Cyprinus carpio (Accession # P24985) and Cytochrome c oxidase (Subunit 1) of Tubifex tubifex (Accession # Q7YAA6) was conducted. The model structure was improved further with 3Drefine, and the final 3D structure was verified with PROCHEK and ERRATA. The physiochemical, as well as the stereochemical parameters of the modelled protein, were evaluated using various tools like ExPASy’s ProtParam, Hydropathy Analysis and EMBOSS pepwheel. The projected model was then docked with toxic ligands, Sodium dodecyl sulfate (SDS), Cetylpyridinium chloride (CPC), and Sodium laureth sulfate (SLES), whose 3D structures were obtained from the Uniprot database. CPC interacted best with Cytochrome c oxidase subunit 2 of Cyprinus carpio and Cytochrome c oxidase subunit 1 of Tubifex tubifex, according to our findings. Furthermore, in the case of all surfactants, hydrophobic interactions with the active site amino acid residues of the modelled protein were observed to be more common than hydrogen bonds and salt bridges. Molecular simulation studies exhibited that the surfactants alter the structural flexibility of the predicted proteins. Hence it may be inferred that the surfactants might alter the structure and dynamics of Cytochrome c oxidase of both worm and fish.

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Molecular modeling, docking and dynamic simulations of growth hormone receptor (GHR) of Labeo rohita

Cited by 12 publications

References 44 publications

Transcriptome Analysis Reveals Differences in Gene Expression in the Muscle of the Brown-Marbled Grouper (Epinephelus fuscoguttatus) with Different Growth Rates

Transcriptome Analysis Reveals Differences in Gene Expression in the Muscle of the Brown-Marbled Grouper (Epinephelus fuscoguttatus) with Different Growth Rates

The Structural Annotations of The Mir-122 Non-Coding RNA from The Tilapia Fish (Oreochromis niloticus)

Homology Modelling, In Silico Prediction And Characterization Of Cytochrome c oxidase In Cyprinus carpio And Tubifex tubifex And Molecular Docking Studies Between The Modelled Protein And Three Commonly Used Surfactants Sodium Dodecyl Sulphate, Cetylpyridinium Chloride And Sodium Laureth Sulphate

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